AlfalfaGEDB | Msa0053340

M. sativa cultivar zhongmu-4 / Msa0053340

KEGG: -
GO: GO:0000976 GO:0000977 GO:0000981 GO:0001012 GO:0001067 GO:0001085 GO:0001228 GO:0003674 GO:0003676 GO:0003677 GO:0003682 GO:0003690 GO:0003700 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005667 GO:0006139 GO:0006351 GO:0006355 GO:0006357 GO:0006366 GO:0006725 GO:0006807 GO:0008134 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009889 GO:0009891 GO:0009893 GO:0009987 GO:0010467 GO:0010468 GO:0010556 GO:0010557 GO:0010604 GO:0010628 GO:0016070 GO:0018130 GO:0019219 GO:0019222 GO:0019438 GO:0030154 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0032502 GO:0032774 GO:0032991 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043565 GO:0044212 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044424 GO:0044464 GO:0045893 GO:0045935 GO:0045944 GO:0046483 GO:0048518 GO:0048522 GO:0048869 GO:0050789 GO:0050794 GO:0051171 GO:0051173 GO:0051252 GO:0051254 GO:0060255 GO:0065007 GO:0071704 GO:0080090 GO:0090304 GO:0097159 GO:0097659 GO:0140110 GO:1901360 GO:1901362 GO:1901363 GO:1901576 GO:1902680 GO:1903506 GO:1903508 GO:1990837 GO:2000112 GO:2001141
PFAM: PF00320.30

Nr:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score

Swissprot:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0053340	sp\|Q5HZ36\|GAT21_ARATH	54.098	61	25	1	2	59	203	263	9.03e-14	67.8

Trembl:

Query id	Subject id	identity %	alignment length	mis matches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0053340	G7I9Y4	70.000	50	12	1	24	70	185	234	4.74e-15	77.8

TFs/TRs:

Gene ID	Type	Classification
Msa0053340	TF	C2C2-GATA

Protein Kinases:

Gene ID	Type	Classification

Network:

Co-expression Network

Gene1	Gene2	correlation coefficient	p_value	FDR

PPI

Gene1	Gene2	Type

Query id	Subject id	identity %	alignment length	mismatches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0053340	MtrunA17_Chr1g0151461	70.000	50	12	1	24	70	185	234	9.13e-19	77.8
Msa0053340	MtrunA17_Chr1g0151471	57.377	61	23	1	10	70	47	104	6.37e-17	69.3
Msa0053340	MtrunA17_Chr7g0271861	48.276	58	30	0	27	84	23	80	3.53e-16	67.8
Msa0053340	MtrunA17_Chr4g0068031	60.784	51	15	2	28	78	32	77	7.78e-14	62.4
Msa0053340	MtrunA17_Chr2g0299081	81.250	32	6	0	24	55	167	198	1.82e-13	63.5
Msa0053340	MtrunA17_Chr4g0071301	81.818	33	6	0	23	55	189	221	2.17e-12	60.8
Msa0053340	MtrunA17_Chr5g0404131	43.103	58	33	0	3	60	169	226	3.05e-11	57.4
Msa0053340	MtrunA17_Chr1g0199671	67.742	31	10	0	28	58	244	274	6.92e-11	56.6
Msa0053340	MtrunA17_Chr8g0373231	60.606	33	13	0	28	60	127	159	9.62e-11	55.5

Query id	Subject id	identity %	alignment length	mismatches	gap openings	q. start	q. end	s. start	s. end	e-value	bit score
Msa0053340	AT5G56860.1	54.098	61	25	1	2	59	203	263	9.18e-15	67.8
Msa0053340	AT3G16870.1	53.448	58	26	1	28	85	44	100	9.66e-15	65.9
Msa0053340	AT5G49300.1	51.852	54	21	1	12	60	17	70	1.44e-14	64.3
Msa0053340	AT5G26930.1	55.814	43	19	0	28	70	28	70	2.30e-13	60.8
Msa0053340	AT4G26150.1	80.645	31	6	0	27	57	200	230	5.48e-13	62.8
Msa0053340	AT2G18380.1	46.552	58	26	1	7	64	78	130	7.04e-13	61.2
Msa0053340	AT4G16141.1	65.854	41	13	1	28	68	39	78	9.54e-13	60.8
Msa0053340	AT3G06740.1	69.697	33	10	0	28	60	43	75	2.91e-12	58.5
Msa0053340	AT4G36620.1	57.895	38	16	0	28	65	77	114	5.09e-12	59.3
Msa0053340	AT3G50870.1	63.636	33	12	0	28	60	154	186	3.31e-11	57.8

Find 29 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE

CRISPR-Local

CRISPR-Local
sgRNA_sequence	on_target_score	Position	Region
GTGTTAAATACTCTAGCCTT+TGG	0.384107	1_2:-7743372	None:intergenic
GGCAAAAGCTGCTAAAGGTT+TGG	0.385602	1_2:+7743639	Msa0053340:CDS
CCTTTGGAGGAGTGGACCTA+TGG	0.393594	1_2:+7743452	Msa0053340:CDS
CCTTAAACGGAGAAGGAAAA+TGG	0.403851	1_2:+7743618	Msa0053340:CDS
GCAACGCATGTGGCCTTAAA+CGG	0.433689	1_2:+7743605	Msa0053340:CDS
TTTGGATACTCACAAGGAAA+AGG	0.463252	1_2:+7743657	Msa0053340:CDS
TACTCTAGCCTTTGGATATG+TGG	0.466888	1_2:-7743364	None:intergenic
ACTCCTCCAAAGGGGAGTCT+TGG	0.473678	1_2:-7743442	None:intergenic
ACTATAGTGGTTGTAGCAGC+TGG	0.486129	1_2:-7743399	None:intergenic
ACAATCTGAGCAAACTATAG+TGG	0.494689	1_2:-7743412	None:intergenic
CTTTGGAGGAGTGGACCTAT+GGG	0.500407	1_2:+7743453	Msa0053340:CDS
CAACCAAGACTCCCCTTTGG+AGG	0.510410	1_2:+7743439	Msa0053340:CDS
AGACAACCAAGACTCCCCTT+TGG	0.517499	1_2:+7743436	Msa0053340:CDS
TTGGATACTCACAAGGAAAA+GGG	0.521424	1_2:+7743658	Msa0053340:CDS
CATAGGTCCACTCCTCCAAA+GGG	0.525622	1_2:-7743451	None:intergenic
GAGTGGACCTATGGGTCCTA+AGG	0.528357	1_2:+7743461	Msa0053340:CDS
CTAATTACCTTAGGACCCAT+AGG	0.530405	1_2:-7743468	None:intergenic
CCATAGGTCCACTCCTCCAA+AGG	0.542869	1_2:-7743452	None:intergenic
AAGACTCCCCTTTGGAGGAG+TGG	0.565345	1_2:+7743444	Msa0053340:CDS
AGTGGTTGTAGCAGCTGGAA+TGG	0.582766	1_2:-7743394	None:intergenic
AAAATGGCAAAAGCTGCTAA+AGG	0.591042	1_2:+7743634	Msa0053340:CDS
CATGTGGCCTTAAACGGAGA+AGG	0.606403	1_2:+7743611	Msa0053340:CDS
TGGCGAAAGCTCATCATCTG+AGG	0.622295	1_2:+7743684	Msa0053340:CDS
ACTCACAAGGAAAAGGGCAA+TGG	0.626006	1_2:+7743664	Msa0053340:CDS
CAGTCTTTGTGCAACGCATG+TGG	0.630452	1_2:+7743595	Msa0053340:intron
TAAAGGTTTGGATACTCACA+AGG	0.633174	1_2:+7743651	Msa0053340:CDS
TGCTACCACCACATATCCAA+AGG	0.634178	1_2:+7743356	Msa0053340:CDS
TCTAGCCTTTGGATATGTGG+TGG	0.649272	1_2:-7743361	None:intergenic
ATAGGTCCACTCCTCCAAAG+GGG	0.735481	1_2:-7743450	None:intergenic

CRISPR-GE

badsite warning	sgRNA_sequence	Strand	Position	Region	GC_content
!!	ACTGTTTTCATTTACTATCA+CGG	+	chr1_2:7743521-7743540	Msa0053340:intron	25.0%
!	ATAGTTAACATGAAACATGT+TGG	+	chr1_2:7743570-7743589	Msa0053340:intron	25.0%
	AGAGACTATCTAATTACCTT+AGG	-	chr1_2:7743480-7743499	None:intergenic	30.0%
	AAAACAGTAGCGAATAAGTT+GGG	-	chr1_2:7743509-7743528	None:intergenic	30.0%
!	GTGTTAAATACTCTAGCCTT+TGG	-	chr1_2:7743375-7743394	None:intergenic	35.0%
	ACAATCTGAGCAAACTATAG+TGG	-	chr1_2:7743415-7743434	None:intergenic	35.0%
	GAAAACAGTAGCGAATAAGT+TGG	-	chr1_2:7743510-7743529	None:intergenic	35.0%
	AAAATGGCAAAAGCTGCTAA+AGG	+	chr1_2:7743634-7743653	Msa0053340:CDS	35.0%
	TAAAGGTTTGGATACTCACA+AGG	+	chr1_2:7743651-7743670	Msa0053340:CDS	35.0%
	TTTGGATACTCACAAGGAAA+AGG	+	chr1_2:7743657-7743676	Msa0053340:CDS	35.0%
	TTGGATACTCACAAGGAAAA+GGG	+	chr1_2:7743658-7743677	Msa0053340:CDS	35.0%
!	TACTCTAGCCTTTGGATATG+TGG	-	chr1_2:7743367-7743386	None:intergenic	40.0%
	CTAATTACCTTAGGACCCAT+AGG	-	chr1_2:7743471-7743490	None:intergenic	40.0%
!	CCATTTTCCTTCTCCGTTTA+AGG	-	chr1_2:7743621-7743640	None:intergenic	40.0%
	CCTTAAACGGAGAAGGAAAA+TGG	+	chr1_2:7743618-7743637	Msa0053340:CDS	40.0%
	TGCTACCACCACATATCCAA+AGG	+	chr1_2:7743356-7743375	Msa0053340:CDS	45.0%
!	TCTAGCCTTTGGATATGTGG+TGG	-	chr1_2:7743364-7743383	None:intergenic	45.0%
	ACTATAGTGGTTGTAGCAGC+TGG	-	chr1_2:7743402-7743421	None:intergenic	45.0%
	GGCAAAAGCTGCTAAAGGTT+TGG	+	chr1_2:7743639-7743658	Msa0053340:CDS	45.0%
	ACTCACAAGGAAAAGGGCAA+TGG	+	chr1_2:7743664-7743683	Msa0053340:CDS	45.0%
	AGTGGTTGTAGCAGCTGGAA+TGG	-	chr1_2:7743397-7743416	None:intergenic	50.0%
	AGACAACCAAGACTCCCCTT+TGG	+	chr1_2:7743436-7743455	Msa0053340:CDS	50.0%
	ATAGGTCCACTCCTCCAAAG+GGG	-	chr1_2:7743453-7743472	None:intergenic	50.0%
	CATAGGTCCACTCCTCCAAA+GGG	-	chr1_2:7743454-7743473	None:intergenic	50.0%
!	CTTTGGAGGAGTGGACCTAT+GGG	+	chr1_2:7743453-7743472	Msa0053340:CDS	50.0%
	CAGTCTTTGTGCAACGCATG+TGG	+	chr1_2:7743595-7743614	Msa0053340:intron	50.0%
!	GCAACGCATGTGGCCTTAAA+CGG	+	chr1_2:7743605-7743624	Msa0053340:CDS	50.0%
!	CATGTGGCCTTAAACGGAGA+AGG	+	chr1_2:7743611-7743630	Msa0053340:CDS	50.0%
	TGGCGAAAGCTCATCATCTG+AGG	+	chr1_2:7743684-7743703	Msa0053340:CDS	50.0%
	CAACCAAGACTCCCCTTTGG+AGG	+	chr1_2:7743439-7743458	Msa0053340:CDS	55.0%
	ACTCCTCCAAAGGGGAGTCT+TGG	-	chr1_2:7743445-7743464	None:intergenic	55.0%
!	AAGACTCCCCTTTGGAGGAG+TGG	+	chr1_2:7743444-7743463	Msa0053340:CDS	55.0%
	CCATAGGTCCACTCCTCCAA+AGG	-	chr1_2:7743455-7743474	None:intergenic	55.0%
!	CCTTTGGAGGAGTGGACCTA+TGG	+	chr1_2:7743452-7743471	Msa0053340:CDS	55.0%
	GAGTGGACCTATGGGTCCTA+AGG	+	chr1_2:7743461-7743480	Msa0053340:CDS	55.0%

Chromosome	Type	Strat	End	Strand	Name
chr1_2	gene	7743342	7743717	7743342	ID=Msa0053340;Name=Msa0053340
chr1_2	mRNA	7743342	7743717	7743342	ID=Msa0053340-mRNA-1;Parent=Msa0053340;Name=Msa0053340-mRNA-1;_AED=0.46;_eAED=0.49;_QI=0\|0\|0\|1\|1\|1\|2\|0\|86
chr1_2	exon	7743342	7743482	7743342	ID=Msa0053340-mRNA-1:exon:2683;Parent=Msa0053340-mRNA-1
chr1_2	exon	7743598	7743717	7743598	ID=Msa0053340-mRNA-1:exon:2684;Parent=Msa0053340-mRNA-1
chr1_2	CDS	7743342	7743482	7743342	ID=Msa0053340-mRNA-1:cds;Parent=Msa0053340-mRNA-1
chr1_2	CDS	7743598	7743717	7743598	ID=Msa0053340-mRNA-1:cds;Parent=Msa0053340-mRNA-1

Gene Sequence	>Msa0053340 ATGAAGAACACAACTGCTACCACCACATATCCAAAGGCTAGAGTATTTAACACCATTCCAGCTGCTACAACCACTATAGTTTGCTCAGATTGTGAGACAACCAAGACTCCCCTTTGGAGGAGTGGACCTATGGGTCCTAAGTCTTTGTGCAACGCATGTGGCCTTAAACGGAGAAGGAAAATGGCAAAAGCTGCTAAAGGTTTGGATACTCACAAGGAAAAGGGCAATGGCGAAAGCTCATCATCTGAGGATGTGAAGTAG
Protein sequence	>Msa0053340 MKNTTATTTYPKARVFNTIPAATTTIVCSDCETTKTPLWRSGPMGPKSLCNACGLKRRRKMAKAAKGLDTHKEKGNGESSSSEDVK*